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Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU281445
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 287 0.18 M Sodium fluoride, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.93 36.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.14 α = 71.26 b = 52.77 β = 85.82 c = 70.57 γ = 64.46
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 66.63 97.7 0.052 0.033 0.991 12.3 3.4 46068
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 96.5 0.492 0.305 0.866 2.4 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6UJ5 1.9 66.63 46068 2332 97.71 0.1825 0.1802 0.1874 0.2271 0.2283 RANDOM 31.491
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 2.09 -0.04 -0.66 -1.64 1.15 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.221 r_dihedral_angle_4_deg 14.999 r_dihedral_angle_3_deg 13.67 r_dihedral_angle_1_deg 6.544 r_angle_refined_deg 1.504 r_angle_other_deg 1.344 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.221 r_dihedral_angle_4_deg 14.999 r_dihedral_angle_3_deg 13.67 r_dihedral_angle_1_deg 6.544 r_angle_refined_deg 1.504 r_angle_other_deg 1.344 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5121 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing